| 1 : |
agomez |
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#include "predatorpreyprinter.h" |
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#include "predatorpreyaggregator.h" |
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#include "areatime.h" |
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#include "readword.h" |
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#include "readaggregation.h" |
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#include "errorhandler.h" |
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#include "predator.h" |
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#include "stockprey.h" |
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#include "gadget.h" |
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#include "runid.h" |
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#include "global.h" |
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PredatorPreyPrinter::PredatorPreyPrinter(CommentStream& infile, const TimeClass* const TimeInfo)
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: Printer(PREDATORPREYPRINTER), aggregator(0), alptr(0), dptr(0) {
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char text[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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//read in the predator names
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int i = 0;
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infile >> text >> ws;
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if (strcasecmp(text, "predatornames") != 0)
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handle.logFileUnexpected(LOGFAIL, "predatornames", text);
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infile >> text >> ws;
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while (!infile.eof() && (strcasecmp(text, "preynames") != 0)) {
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predatornames.resize(new char[strlen(text) + 1]);
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strcpy(predatornames[i++], text);
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infile >> text >> ws;
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}
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if (predatornames.Size() == 0)
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handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - failed to read predators");
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handle.logMessage(LOGMESSAGE, "Read predator data - number of predators", predatornames.Size());
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//read in the prey names
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i = 0;
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infile >> text >> ws;
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while (!infile.eof() && (strcasecmp(text, "areaaggfile") != 0)) {
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preynames.resize(new char[strlen(text) + 1]);
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strcpy(preynames[i++], text);
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infile >> text >> ws;
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}
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if (preynames.Size() == 0)
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handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - failed to read preys");
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handle.logMessage(LOGMESSAGE, "Read prey data - number of preys", preynames.Size());
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//read in area aggregation from file
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filename = new char[MaxStrLength];
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strncpy(filename, "", MaxStrLength);
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ifstream datafile;
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CommentStream subdata(datafile);
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infile >> filename >> ws;
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datafile.open(filename, ios::in);
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handle.checkIfFailure(datafile, filename);
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handle.Open(filename);
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i = readAggregation(subdata, areas, areaindex);
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handle.Close();
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datafile.close();
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datafile.clear();
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//read in age aggregation from file
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readWordAndValue(infile, "ageaggfile", filename);
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datafile.open(filename, ios::in);
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handle.checkIfFailure(datafile, filename);
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handle.Open(filename);
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i = readAggregation(subdata, ages, ageindex);
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handle.Close();
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datafile.close();
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datafile.clear();
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//read in length aggregation from file
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DoubleVector lengths;
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readWordAndValue(infile, "lenaggfile", filename);
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datafile.open(filename, ios::in);
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handle.checkIfFailure(datafile, filename);
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handle.Open(filename);
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i = readLengthAggregation(subdata, lengths, lenindex);
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handle.Close();
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datafile.close();
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datafile.clear();
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LgrpDiv = new LengthGroupDivision(lengths);
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if (LgrpDiv->Error())
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handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - failed to create length group");
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//open the printfile
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readWordAndValue(infile, "printfile", filename);
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outfile.open(filename, ios::out);
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handle.checkIfFailure(outfile, filename);
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infile >> text >> ws;
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if (strcasecmp(text, "precision") == 0) {
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infile >> precision >> ws >> text >> ws;
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width = precision + 4;
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} else {
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// use default values
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precision = largeprecision;
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width = largewidth;
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}
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if (precision < 0)
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handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - invalid value of precision");
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if (strcasecmp(text, "printatstart") == 0)
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infile >> printtimeid >> ws >> text >> ws;
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else
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printtimeid = 0;
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if (printtimeid != 0 && printtimeid != 1)
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handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - invalid value of printatstart");
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if (strcasecmp(text, "yearsandsteps") != 0)
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handle.logFileUnexpected(LOGFAIL, "yearsandsteps", text);
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if (!AAT.readFromFile(infile, TimeInfo))
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handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - wrong format for yearsandsteps");
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//prepare for next printfile component
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infile >> ws;
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if (!infile.eof()) {
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infile >> text >> ws;
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if (strcasecmp(text, "[component]") != 0)
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handle.logFileUnexpected(LOGFAIL, "[component]", text);
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}
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//finished initializing. Now print first lines
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outfile << "; ";
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RUNID.Print(outfile);
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outfile << "; Predation output file for the following predators";
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for (i = 0; i < predatornames.Size(); i++)
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outfile << sep << predatornames[i];
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outfile << "\n; Consuming the following preys";
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for (i = 0; i < preynames.Size(); i++)
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outfile << sep << preynames[i];
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if (printtimeid == 0)
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outfile << "\n; Printing the following information at the end of each timestep";
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else
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outfile << "\n; Printing the following information at the start of each timestep";
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outfile << "\n; year-step-area-age-length-number consumed-biomass consumed-mortality\n";
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outfile.flush();
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}
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void PredatorPreyPrinter::setPredAndPrey(PredatorPtrVector& predatorvec,
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PreyPtrVector& preyvec, const AreaClass* const Area) {
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PredatorPtrVector predators;
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PreyPtrVector preys;
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int i, j, k, found, minage, maxage;
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delete aggregator;
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for (i = 0; i < predatorvec.Size(); i++)
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for (j = 0; j < predatornames.Size(); j++)
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if (strcasecmp(predatorvec[i]->getName(), predatornames[j]) == 0)
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predators.resize(predatorvec[i]);
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if (predators.Size() != predatornames.Size()) {
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handle.logMessage(LOGWARN, "Error in predatorpreyprinter - failed to match predators");
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for (i = 0; i < predatorvec.Size(); i++)
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handle.logMessage(LOGWARN, "Error in predatorpreyprinter - found predator", predatorvec[i]->getName());
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for (i = 0; i < predatornames.Size(); i++)
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handle.logMessage(LOGWARN, "Error in predatorpreyprinter - looking for predator", predatornames[i]);
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handle.logMessage(LOGFAIL, ""); //JMB this will exit gadget
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}
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for (i = 0; i < predators.Size(); i++)
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for (j = 0; j < predators.Size(); j++)
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if ((strcasecmp(predators[i]->getName(), predators[j]->getName()) == 0) && (i != j))
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handle.logMessage(LOGFAIL, "Error in predatorpreyprinter - repeated predator", predators[i]->getName());
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for (i = 0; i < preyvec.Size(); i++)
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for (j = 0; j < preynames.Size(); j++)
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if (strcasecmp(preyvec[i]->getName(), preynames[j]) == 0)
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preys.resize(preyvec[i]);
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if (preys.Size() != preynames.Size()) {
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handle.logMessage(LOGWARN, "Error in predatorpreyprinter - failed to match preys");
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for (i = 0; i < preyvec.Size(); i++)
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handle.logMessage(LOGWARN, "Error in predatorpreyprinter - found prey", preyvec[i]->getName());
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for (i = 0; i < preynames.Size(); i++)
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handle.logMessage(LOGWARN, "Error in predatorpreyprinter - looking for prey", preynames[i]);
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handle.logMessage(LOGFAIL, ""); //JMB this will exit gadget
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}
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for (i = 0; i < preys.Size(); i++)
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for (j = 0; j < preys.Size(); j++)
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if ((strcasecmp(preys[i]->getName(), preys[j]->getName()) == 0) && (i != j))
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handle.logMessage(LOGFAIL, "Error in predatorpreyprinter - repeated prey", preys[i]->getName());
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//check that the preys are stocks and not otherfood
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for (i = 0; i < preys.Size(); i++)
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if (preys[i]->getType() == LENGTHPREY)
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handle.logMessage(LOGFAIL, "Error in predatorpreyprinter - cannot print prey", preys[i]->getName());
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//change from outer areas to inner areas.
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for (i = 0; i < areas.Nrow(); i++)
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for (j = 0; j < areas.Ncol(i); j++)
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areas[i][j] = Area->getInnerArea(areas[i][j]);
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//check predator and prey areas, ages and length groups
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if (handle.getLogLevel() >= LOGWARN) {
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for (j = 0; j < areas.Nrow(); j++) {
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found = 0;
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for (i = 0; i < predators.Size(); i++)
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for (k = 0; k < areas.Ncol(j); k++)
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if (predators[i]->isInArea(areas[j][k]))
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found++;
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if (found == 0)
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handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - predators not defined on all areas");
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}
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for (j = 0; j < areas.Nrow(); j++) {
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found = 0;
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for (i = 0; i < preys.Size(); i++)
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for (k = 0; k < areas.Ncol(j); k++)
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if (preys[i]->isInArea(areas[j][k]))
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found++;
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if (found == 0)
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handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - preys not defined on all areas");
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}
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minage = 9999;
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maxage = -1;
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for (i = 0; i < ages.Nrow(); i++) {
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for (j = 0; j < ages.Ncol(i); j++) {
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minage = min(ages[i][j], minage);
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maxage = max(ages[i][j], maxage);
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}
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}
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found = 0;
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for (i = 0; i < preys.Size(); i++)
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if (minage >= ((StockPrey*)preys[i])->minAge())
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found++;
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if (found == 0)
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handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - minimum age less than prey age");
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found = 0;
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for (i = 0; i < preys.Size(); i++)
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if (maxage <= ((StockPrey*)preys[i])->maxAge())
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found++;
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if (found == 0)
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handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - maximum age greater than prey age");
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found = 0;
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| 247 : |
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for (i = 0; i < preys.Size(); i++)
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| 248 : |
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if (LgrpDiv->maxLength(0) > preys[i]->getLengthGroupDiv()->minLength())
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found++;
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| 250 : |
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if (found == 0)
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| 251 : |
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handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - minimum length group less than prey length");
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found = 0;
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| 254 : |
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for (i = 0; i < preys.Size(); i++)
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if (LgrpDiv->minLength(LgrpDiv->numLengthGroups()) < preys[i]->getLengthGroupDiv()->maxLength())
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| 256 : |
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found++;
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| 257 : |
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if (found == 0)
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| 258 : |
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handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - maximum length group greater than prey length");
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| 259 : |
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}
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| 260 : |
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| 261 : |
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aggregator = new PredatorPreyAggregator(predators, preys, LgrpDiv, areas, ages);
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| 262 : |
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}
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| 263 : |
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| 264 : |
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void PredatorPreyPrinter::Print(const TimeClass* const TimeInfo, int printtime) {
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| 265 : |
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| 266 : |
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if ((!AAT.atCurrentTime(TimeInfo)) || (printtime != printtimeid))
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| 267 : |
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return;
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| 268 : |
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| 269 : |
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int a, age, len;
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| 270 : |
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aggregator->Sum(TimeInfo);
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| 271 : |
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alptr = &aggregator->getConsumption();
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| 272 : |
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for (a = 0; a < areas.Nrow(); a++) {
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| 273 : |
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dptr = aggregator->getMortality()[a];
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| 274 : |
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for (age = (*alptr)[a].minAge(); age <= (*alptr)[a].maxAge(); age++) {
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| 275 : |
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for (len = (*alptr)[a].minLength(age); len < (*alptr)[a].maxLength(age); len++) {
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| 276 : |
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outfile << setw(lowwidth) << TimeInfo->getYear() << sep
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| 277 : |
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<< setw(lowwidth) << TimeInfo->getStep() << sep
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| 278 : |
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<< setw(printwidth) << areaindex[a] << sep
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| 279 : |
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<< setw(printwidth) << ageindex[age] << sep
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| 280 : |
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<< setw(printwidth) << lenindex[len] << sep;
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| 281 : |
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| 282 : |
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//JMB crude filter to remove the 'silly' values from the output
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| 283 : |
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if (((*alptr)[a][age][len].N < rathersmall) || ((*alptr)[a][age][len].W < 0.0))
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| 284 : |
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outfile << setw(width) << 0 << sep << setw(width) << 0 << sep << setw(width) << 0 << endl;
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| 285 : |
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else
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| 286 : |
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outfile << setprecision(precision) << setw(width) << (*alptr)[a][age][len].N
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| 287 : |
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<< sep << setprecision(precision) << setw(width)
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| 288 : |
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<< (*alptr)[a][age][len].N * (*alptr)[a][age][len].W
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| 289 : |
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<< sep << setprecision(precision) << setw(width)
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| 290 : |
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<< (*dptr)[age][len] << endl;
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| 291 : |
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}
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| 292 : |
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}
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| 293 : |
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}
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| 294 : |
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outfile.flush();
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| 295 : |
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}
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| 296 : |
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| 297 : |
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PredatorPreyPrinter::~PredatorPreyPrinter() {
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| 298 : |
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outfile.close();
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| 299 : |
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outfile.clear();
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| 300 : |
|
|
delete LgrpDiv;
|
| 301 : |
|
|
delete aggregator;
|
| 302 : |
|
|
int i;
|
| 303 : |
|
|
for (i = 0; i < predatornames.Size(); i++)
|
| 304 : |
|
|
delete[] predatornames[i];
|
| 305 : |
|
|
for (i = 0; i < preynames.Size(); i++)
|
| 306 : |
|
|
delete[] preynames[i];
|
| 307 : |
|
|
for (i = 0; i < lenindex.Size(); i++)
|
| 308 : |
|
|
delete[] lenindex[i];
|
| 309 : |
|
|
for (i = 0; i < ageindex.Size(); i++)
|
| 310 : |
|
|
delete[] ageindex[i];
|
| 311 : |
|
|
for (i = 0; i < areaindex.Size(); i++)
|
| 312 : |
|
|
delete[] areaindex[i];
|
| 313 : |
|
|
}
|
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